The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3.

A three-body scattering process in the presence of Coulomb interaction can be decomposed formally into a two-body single channel, a two-body multichannel and a genuine three-body scattering. The corresponding integral equations are coupled Lippmann-Schwinger and Faddeev-Merkuriev integral equations. We solve them by applying the Coulomb-Sturmian separable expansion method. We present elastic scattering and reaction cross sections of the e + + H system both below and above the H(n = 2) threshold. We found excellent agreements with previous calculations in most cases. PACS number(s): 34.10.+x, 34.85.+x, 21.45.+v, 03.65.Nk, 02.30.Rz, 02.60.Nm The three-body Coulomb scattering problem is one of the most challenging long-standing problems of nonrelativistic quantum mechanics. The source of the difficulties is related to the long-range character of the Coulomb potential. In the standard scattering theory it is supposed that the particles move freely asymptotically. That is not the case if Coulombic interactions are involved. As a result the fundamental equations of the three-body problems, the Faddeev-equations, become illbehaved if they are applied for Coulomb potentials in a straightforward manner.The first, and formally exact, approach was proposed by Noble [1]. His formulation was designed for solving the nuclear three-body Coulomb problem, where all Coulomb interactions are repulsive. The interactions were split into short-range and long-range Coulomb-like parts and the long-range parts were formally included in the "free" Green's operator. Therefore the corresponding Faddeev-Noble equations become mathematically wellbehaved and in the absence of Coulomb interaction they fall back to the standard equations. However, the associated Green's operator is not known. This formalism, as presented at that time, was not suitable for practical calculations.In Noble's approach the separation of the Coulomb-like potential into short-range and long-range parts were carried out in the two-body configuration space. Merkuriev extended the idea of Noble by performing the splitting in the three-body configuration space. This was a crucial development since it made possible to treat attractive Coulomb interactions on an equal footing as repulsive ones. This theory has been developed using integral equations with connected (compact) kernels and transformed into configuration-space differential equations with asymptotic boundary conditions [2]. In practical calculations, so far only the latter version of the theory has been considered. The primary reason is that the more complicated structure of the Green's operators in the kernels of the Faddeev-Merkuriev integral equations has not yet allowed any direct solution. However, use of integral equations is a very appealing approach since no boundary conditions are required.Recently, one of us has developed a novel method for treating the three-body problem with repulsive Coulomb interactions in three-potential picture [3]. In this approach a three-body Coulomb scattering process can ...

A bipolar spherical harmonics expansion of the modified Faddeev equation is used to calculate the K-matrices of the e++H scattering for up to five open channels and for total angular momentum L4. Partial cross sections and differential cross sections including hydrogen production channels are reported. Comparison with previous calculations are made whenever feasible. Good agreement is observed.

Using a recently developed approach for treating the three-dimensional anisotropic scattering we find considerable influence of a nonresonant laser field with intensity I> or =10(5) W/cm(2) on the Cs-Cs ultracold collisions. Strong dependence on the laser wavelength lambda(L) is shown at the optical region as lambda(L) becomes shorter than the critical value lambda(0) approximately 3000 nm (of the atomic de Broglie wave lambda) defining the region lambda(0)< or =lambda of the s-wave domination in the absence of the external field. Dependence on the laser polarization is also essential. The found effect can be applicable for controlling atom-atom interactions at ultralow temperatures.

No abstract